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EMBL BioImage Data Analysis



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Yoshikatsu Sato, the head of microscope facility @NagoyaITbM presenting practicals #EMBOLivePlant
About 18 hours, 31 mins ago by: Kota Miura (@cmci_)

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Miyo Terao Morita showing analysis of gravitropism using centrifuge microscope they newly developed. I only know…
About 19 hours, 3 mins ago by: Kota Miura (@cmci_)

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@KeikoUTorii ... which then became the cover page of Development cell. convincing.
About 20 hours ago by: Kota Miura (@cmci_)

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@KeikoUTorii model-based hypothesis lead to experiment results with single guard cell development or multiple >2 gu…
About 20 hours, 8 mins ago by: Kota Miura (@cmci_)

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now, @KeikoUTorii on stomata development - how very specific cell fate decisions are made, with proper spacing bet…
About 20 hours, 25 mins ago by: Kota Miura (@cmci_)

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@YvonJaillais talk on nanoclustering of ROP6, great analyses using various approaches to assess protein mobility…
About 20 hours, 41 mins ago by: Kota Miura (@cmci_)
Algorithm FRAP Fiji ImageJ ImageJ Plugin ImageJ Plugin 3Dviewer Imaris Java Javascript Python R added 201904 Freiburg bias blog dokuwiki fiji google imagej java libraries matlab meetings neubias news papers python references software webadmin

CMCI weblog

Photobleaching Correction -3D time series

There are several IJ tools available for 2D time series bleaching correction, but seems not with 3D:

2D-t tools:

    • Phair's double normalization method. Dependent on ratio, similar to the above, but can specify reference area (if my understanding is correct).
    • proposes two ways,
      1. conceptually similar to above two: estimate the correction ratio. But this is done by fitting exponential decay curve and use decay parameter.
        1. <jsm> I_c(t) = I(t) / exp^{-\tau t}</jsm>
      2. use “enhance contrast”. framewise Histogram streching.

Among these, exponential decay method is theoretically clean (but in practice, timeseries are not teoretical…).

Anycase, there should be 3D-t bleach correction tool (and I need it NOW). I might make some quick solution using two methods, one using division of first frame and the other with exponential fitting.

By the way, bleaching corrected images cannot basically be used for intensity quantification (FRAP, on the other hands, correct bleaching after measuring the raw image). If you are analyzing shapes or positions, no problem for quantification.

here is the “ratio” version:

macro "Bleach Corection 3D-t by ratio"{
	run("Duplicate...", "title=bleach_corrected duplicate");
	getDimensions(width, height, channels, slices, frames);
	if (frames == 1) {
		uslices = getNumber("how many z slices/timepoint?", 1);
		if ((slices%uslices) !=0) exit("that slice number dows not match with the current stack");
		frames = slices / uslices;
	tIntA = newArray(frames);
	for(i=0; i<frames; i++){
		startf = (i*slices)+1;
		endf = (i+1)*slices;
		op ="start="+startf+" stop="+endf+" projection=[Sum Slices]";
		run("Z Project...", op);
		getRawStatistics(nPixels, mean);
		if (i==0) tIntA[i] = mean;
		else tIntA[i] = mean/tIntA[0];
	setBatchMode("exit and display");
	tIntA[0] =1;
	for(i=0; i<frames; i++){
		for(j=0; j<slices; j++){
			curframe = i*slices + j+1;
			//print("frame"+curframe + " factor" + tIntA[i]);
			op = "value="+tIntA[i]+" slice";
			run("Divide...", op);
		print("time point:"+i+1 + "  factor" + tIntA[i]);

Before Correction (each row is a time point, with 8 z-slices)
 Before each row is a time point Average intensity along stack slices. 5 peaks corresponds to 5 time points. Before

After Correction
After After

DeadEasy Caspase ImageJ plugin

There are often cases I see that ImageJ plugins that seems to be very useful is not linked to ImageJ plugin site. Here is one case, I just happened to find.

DeadEasy Caspase ImageJ plugin

“Here, we present a method based on image filtering and mathematical morphology techniques, to count automatically the number of dying cells in intact fruit-fly embryos. We call the resulting programme DeadEasy Caspase. It has been validated for Drosophila and we present examples of its power to address biological questions. Quantification is automatic, accurate, objective, and very fast.”

description is

Lecture Notes: FRAP internal course

Lecture Notes: FRAP internal course is now available (not completed yet but…). More will be added by Sebastian Huet and Christian Tischer later on.

jsMath plugin installed

Installed jsMath plugin, for using tex code directly in this wiki. Some problems seems to appear with previous text with .htaccess codes, but will fix later.

further notes: 2010 Apr. 21
I initially used jsMath to show math equations but then realized that mathJax is more up-to-date module for doing this (mathJax actually is de facto jsMath2.0). I then switched to mathJax.

MathJax works well with Chrome when you view this page. But then soon I found out that this is possible with only Chrome, not with Firefox nor IE. Since most of people visiting this site use Firefox, I started to try configuring but did not work with many different trials… then finally I found a solution for Firefox; upgrade it. The problem I had in viewing math equation was occurring with version 3.0x (on win32), and this does not happen and works well when version 3.6.3 is used. It was as simple as that. without thoughts, I was thinking that “My Firefox should be pretty new”.

The problem I encountered seems to be due to difference in the web-font loading settings. With IE, one better try to use at least IE9. I have not tired this yet, and probably will not because I have not seen any visitor using IE these days.

By the way, if you want to test if your browser is enabled with viewing math equation in, click the link below to test if it is possible.


a disadvantage after installing jsMath plugin is that the page loading became significantly slower than before.

Blocking spam

There has been Spam comments rushing in so I set the comments to be only available through CAPTCHA.

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Weblog Archive

blogtng/blogtop.txt · Last modified: 2016/05/24 05:46 (external edit)